\[\Delta CpG = res_{dex} − res_{base}\]
\[res_{base} \sim CpG_{base} − (\beta_0 + \beta_{1−9} \times Cov)\]
\[res_{dex} \sim CpG_{dex} − (\beta_0 + \beta_{1−9} \times Cov)\]
Cov = {Sex, Age, BMI, MDD Status, SmokingScore, SV, PC}
where
Smoking Score: smoking score estimated from DNAm data using Elliot's CpGs
SV: first three significant Surrogate Variables calculated based on DNAm
PC: first two significant PCs computed using genotype data and PLINK MDS method
ggplot(bcc.melt.df, aes(x = variable, y = value, fill = Treatment)) + geom_boxplot(alpha = 0.2, aes(color = Treatment)) +
theme(legend.position = "bottom", legend.title = element_blank(), panel.grid.major = element_blank(),
panel.background = element_blank(), plot.title = element_text(size = 10), axis.title = element_text(size = 10),
axis.text.x = element_text(angle = 45, hjust = 1)) + labs(x = " ", y = "Cellular proportion estimates") +
scale_fill_manual(values = cbPalette) + scale_color_manual(values = cbPalette)
ggplot(bcc.abs.delta.melt.df, aes(x = variable, y = value)) + geom_boxplot(alpha = 0.2) + geom_hline(yintercept = 0,
color = "red", size = 0.2) + theme(legend.position = "bottom", legend.title = element_blank(), panel.grid.major = element_blank(),
panel.background = element_blank(), plot.title = element_text(size = 10), axis.title = element_text(size = 10),
axis.text.x = element_text(angle = 45, hjust = 1)) + labs(x = " ", y = "Absolute change in BBCs after GR-stimulation")
y <- "Bas"
ylab <- "Basophils"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Neu"
ylab <- "Neutrophils"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Eos"
ylab <- "Eosonphils"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Mono"
ylab <- "Monocytes"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "NK"
ylab <- "Natural Killer"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Treg"
ylab <- "T Regulatory"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "CD4mem"
ylab <- "Memory CD4T Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "CD4nv"
ylab <- "Naive CD4T Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "CD8mem"
ylab <- "Memory CD8T Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "CD8nv"
ylab <- "Naive CD8T Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Bmem"
ylab <- "Memory B Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))
y <- "Bnv"
ylab <- "Naive B Cells"
base.plt <- ggscatterstats(data = base.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = base.plt.title)
dex.plt <- ggscatterstats(data = dex.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE, ylab = ylab,
xlab = xlab, title = dex.plt.title)
delta.plt <- ggscatterstats(data = delta.df, x = EpiStressScore, y = !!ensym(y), bf.message = FALSE,
ylab = ylab, xlab = xlab, title = delta.plt.title)
delta.sc.base.bcc.plt <- ggscatterstats(data = delta.score.base.bcc.df, x = EpiStressScore, y = !!ensym(y),
bf.message = FALSE, ylab = ylab, xlab = xlab, title = delta.sc.base.bcc.plt.title)
grid.arrange(arrangeGrob(base.plt, delta.sc.base.bcc.plt, ncol = 2))
grid.arrange(arrangeGrob(dex.plt, delta.plt, ncol = 2))